Cobalt in PDB 3qzp: Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX

The structure of Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX, PDB code: 3qzp was solved by J.C.Grigg, C.X.Mao, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.465, 51.707, 55.747, 90.00, 92.08, 90.00
R / Rfree (%)	17.8 / 22.3

The binding sites of Cobalt atom in the Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX (pdb code 3qzp). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX, PDB code: 3qzp:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX within 5.0Å range: probe atom residue distance (Å) B Occ A:Co200 b:14.8 occ:0.50 CO A:COH200 0.0 14.8 0.5 CO A:COH200 0.1 10.4 0.5 ND A:COH200 1.9 10.9 0.5 NA A:COH200 2.0 14.5 0.5 NC A:COH200 2.0 8.8 0.5 ND A:COH200 2.0 14.2 0.5 NC A:COH200 2.0 13.6 0.5 NB A:COH200 2.0 14.5 0.5 NA A:COH200 2.0 9.0 0.5 NB A:COH200 2.0 9.2 0.5 NE2 A:HIS83 2.3 11.9 1.0 OH A:TYR166 2.4 24.1 1.0 C1D A:COH200 3.0 10.8 0.5 C4D A:COH200 3.0 11.1 0.5 C4D A:COH200 3.1 14.2 0.5 C4C A:COH200 3.1 13.2 0.5 C4B A:COH200 3.1 15.0 0.5 C4C A:COH200 3.1 9.0 0.5 C1C A:COH200 3.1 13.6 0.5 C1A A:COH200 3.1 15.7 0.5 C4A A:COH200 3.1 8.1 0.5 C1B A:COH200 3.1 14.5 0.5 C1D A:COH200 3.1 12.8 0.5 C1B A:COH200 3.1 9.4 0.5 C1A A:COH200 3.1 9.3 0.5 C1C A:COH200 3.1 8.9 0.5 C4B A:COH200 3.1 9.4 0.5 C4A A:COH200 3.1 15.0 0.5 CD2 A:HIS83 3.2 12.1 1.0 CE1 A:HIS83 3.3 13.6 1.0 CZ A:TYR166 3.4 26.5 1.0 CHD A:COH200 3.5 10.8 0.5 CHA A:COH200 3.5 14.7 0.5 CHC A:COH200 3.5 14.3 0.5 CHA A:COH200 3.5 9.5 0.5 CHD A:COH200 3.5 12.1 0.5 CHB A:COH200 3.5 7.4 0.5 CHB A:COH200 3.6 15.0 0.5 CHC A:COH200 3.6 7.1 0.5 CE1 A:TYR166 4.0 26.2 1.0 OH A:TYR170 4.2 21.3 1.0 CE2 A:TYR166 4.3 26.0 1.0 C3C A:COH200 4.3 12.3 0.5 C2D A:COH200 4.3 12.1 0.5 C3D A:COH200 4.3 13.4 0.5 C3C A:COH200 4.3 10.8 0.5 C3B A:COH200 4.3 14.9 0.5 C3D A:COH200 4.3 14.0 0.5 C2D A:COH200 4.4 13.3 0.5 C2C A:COH200 4.4 13.0 0.5 C3B A:COH200 4.4 9.6 0.5 C3A A:COH200 4.4 8.3 0.5 C2B A:COH200 4.4 15.7 0.5 C2A A:COH200 4.4 17.6 0.5 C2A A:COH200 4.4 9.1 0.5 C2C A:COH200 4.4 9.1 0.5 C3A A:COH200 4.4 16.3 0.5 C2B A:COH200 4.4 9.3 0.5 CG A:HIS83 4.4 10.8 1.0 ND1 A:HIS83 4.4 11.4 1.0 CE2 A:TYR170 4.5 17.8 1.0 CZ A:TYR170 4.6 20.2 1.0

Cobalt binding site 2 out of 4 in the Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX within 5.0Å range: probe atom residue distance (Å) B Occ A:Co200 b:10.4 occ:0.50 CO A:COH200 0.0 10.4 0.5 CO A:COH200 0.1 14.8 0.5 ND A:COH200 1.9 14.2 0.5 NB A:COH200 1.9 9.2 0.5 NC A:COH200 2.0 13.6 0.5 NA A:COH200 2.0 9.0 0.5 ND A:COH200 2.0 10.9 0.5 NC A:COH200 2.0 8.8 0.5 NA A:COH200 2.0 14.5 0.5 NB A:COH200 2.0 14.5 0.5 NE2 A:HIS83 2.2 11.9 1.0 OH A:TYR166 2.5 24.1 1.0 C4C A:COH200 3.0 13.2 0.5 C4D A:COH200 3.0 14.2 0.5 C4A A:COH200 3.1 8.1 0.5 C1B A:COH200 3.1 9.4 0.5 C1D A:COH200 3.1 12.8 0.5 C1C A:COH200 3.1 13.6 0.5 C4B A:COH200 3.1 9.4 0.5 C4D A:COH200 3.1 11.1 0.5 C1D A:COH200 3.1 10.8 0.5 C4B A:COH200 3.1 15.0 0.5 CD2 A:HIS83 3.1 12.1 1.0 C1C A:COH200 3.1 8.9 0.5 C1A A:COH200 3.1 9.3 0.5 C4C A:COH200 3.1 9.0 0.5 C1A A:COH200 3.1 15.7 0.5 C1B A:COH200 3.1 14.5 0.5 C4A A:COH200 3.2 15.0 0.5 CE1 A:HIS83 3.2 13.6 1.0 CHD A:COH200 3.5 12.1 0.5 CHB A:COH200 3.5 7.4 0.5 CZ A:TYR166 3.5 26.5 1.0 CHA A:COH200 3.5 14.7 0.5 CHC A:COH200 3.5 14.3 0.5 CHD A:COH200 3.5 10.8 0.5 CHA A:COH200 3.6 9.5 0.5 CHC A:COH200 3.6 7.1 0.5 CHB A:COH200 3.6 15.0 0.5 CE1 A:TYR166 4.1 26.2 1.0 C3C A:COH200 4.3 12.3 0.5 CG A:HIS83 4.3 10.8 1.0 ND1 A:HIS83 4.3 11.4 1.0 C3D A:COH200 4.3 14.0 0.5 C2C A:COH200 4.3 13.0 0.5 C3B A:COH200 4.3 9.6 0.5 C2D A:COH200 4.3 13.3 0.5 C3A A:COH200 4.3 8.3 0.5 C3B A:COH200 4.3 14.9 0.5 C3D A:COH200 4.3 13.4 0.5 C2D A:COH200 4.4 12.1 0.5 C3C A:COH200 4.4 10.8 0.5 C2B A:COH200 4.4 9.3 0.5 OH A:TYR170 4.4 21.3 1.0 C2A A:COH200 4.4 9.1 0.5 C2B A:COH200 4.4 15.7 0.5 C2C A:COH200 4.4 9.1 0.5 C2A A:COH200 4.4 17.6 0.5 C3A A:COH200 4.4 16.3 0.5 CE2 A:TYR166 4.4 26.0 1.0 CE2 A:TYR170 4.6 17.8 1.0 CZ A:TYR170 4.7 20.2 1.0

Cobalt binding site 3 out of 4 in the Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:15.8 occ:0.50 CO B:COH201 0.0 15.8 0.5 CO B:COH201 0.2 9.9 0.5 ND B:COH201 1.9 12.7 0.5 NC B:COH201 2.0 9.4 0.5 NC B:COH201 2.0 14.8 0.5 NB B:COH201 2.0 15.1 0.5 NA B:COH201 2.0 17.1 0.5 ND B:COH201 2.0 16.8 0.5 NA B:COH201 2.0 10.5 0.5 NB B:COH201 2.0 10.2 0.5 NE2 B:HIS83 2.3 12.8 1.0 OH B:TYR166 2.4 22.3 1.0 C4C B:COH201 3.0 10.1 0.5 C1D B:COH201 3.0 12.2 0.5 C4D B:COH201 3.1 12.7 0.5 C1B B:COH201 3.1 15.0 0.5 C4B B:COH201 3.1 15.3 0.5 C4A B:COH201 3.1 16.5 0.5 C1C B:COH201 3.1 9.6 0.5 C4D B:COH201 3.1 16.7 0.5 C4C B:COH201 3.1 15.1 0.5 C4B B:COH201 3.1 9.9 0.5 C1D B:COH201 3.1 15.9 0.5 C1C B:COH201 3.1 14.6 0.5 C1B B:COH201 3.1 10.2 0.5 C1A B:COH201 3.1 10.8 0.5 C1A B:COH201 3.1 17.5 0.5 C4A B:COH201 3.1 10.2 0.5 CE1 B:HIS83 3.2 13.0 1.0 CD2 B:HIS83 3.3 12.2 1.0 CZ B:TYR166 3.4 26.3 1.0 CHD B:COH201 3.5 11.1 0.5 CHB B:COH201 3.5 15.0 0.5 CHA B:COH201 3.5 11.9 0.5 CHC B:COH201 3.5 8.6 0.5 CHA B:COH201 3.5 17.3 0.5 CHC B:COH201 3.5 14.2 0.5 CHD B:COH201 3.6 15.0 0.5 CHB B:COH201 3.6 9.5 0.5 CE1 B:TYR166 3.9 26.4 1.0 OH B:TYR170 4.1 22.9 1.0 C3C B:COH201 4.3 10.0 0.5 C2D B:COH201 4.3 14.0 0.5 CE2 B:TYR166 4.3 26.4 1.0 C3C B:COH201 4.3 14.8 0.5 C3D B:COH201 4.3 15.1 0.5 C3B B:COH201 4.3 15.0 0.5 ND1 B:HIS83 4.3 12.4 1.0 C3B B:COH201 4.3 10.6 0.5 C2B B:COH201 4.4 14.3 0.5 C2C B:COH201 4.4 9.8 0.5 C3A B:COH201 4.4 18.0 0.5 C3D B:COH201 4.4 17.1 0.5 C2D B:COH201 4.4 16.4 0.5 C2C B:COH201 4.4 14.6 0.5 C2A B:COH201 4.4 19.1 0.5 C2B B:COH201 4.4 10.6 0.5 C2A B:COH201 4.4 11.4 0.5 CG B:HIS83 4.4 11.5 1.0 C3A B:COH201 4.4 10.6 0.5 CZ B:TYR170 4.6 23.3 1.0 CE2 B:TYR170 4.6 21.4 1.0

Cobalt binding site 4 out of 4 in the Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Staphylococcus Aureus Isda Neat Domain in Complex with Cobalt- Protoporphyrin IX within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:9.9 occ:0.50 CO B:COH201 0.0 9.9 0.5 CO B:COH201 0.2 15.8 0.5 ND B:COH201 1.9 16.8 0.5 NC B:COH201 1.9 14.8 0.5 NB B:COH201 1.9 10.2 0.5 NA B:COH201 2.0 10.5 0.5 ND B:COH201 2.0 12.7 0.5 NC B:COH201 2.0 9.4 0.5 NA B:COH201 2.0 17.1 0.5 NB B:COH201 2.0 15.1 0.5 NE2 B:HIS83 2.1 12.8 1.0 OH B:TYR166 2.5 22.3 1.0 C4C B:COH201 3.0 15.1 0.5 C1D B:COH201 3.0 15.9 0.5 C4D B:COH201 3.1 16.7 0.5 CE1 B:HIS83 3.1 13.0 1.0 C1B B:COH201 3.1 10.2 0.5 C4B B:COH201 3.1 9.9 0.5 C4D B:COH201 3.1 12.7 0.5 C1D B:COH201 3.1 12.2 0.5 C1A B:COH201 3.1 10.8 0.5 C4C B:COH201 3.1 10.1 0.5 C1C B:COH201 3.1 14.6 0.5 C1C B:COH201 3.1 9.6 0.5 C1B B:COH201 3.1 15.0 0.5 C4A B:COH201 3.1 10.2 0.5 C4B B:COH201 3.1 15.3 0.5 C4A B:COH201 3.1 16.5 0.5 C1A B:COH201 3.1 17.5 0.5 CD2 B:HIS83 3.1 12.2 1.0 CHD B:COH201 3.5 15.0 0.5 CHC B:COH201 3.5 8.6 0.5 CZ B:TYR166 3.5 26.3 1.0 CHA B:COH201 3.5 11.9 0.5 CHA B:COH201 3.5 17.3 0.5 CHB B:COH201 3.5 9.5 0.5 CHB B:COH201 3.5 15.0 0.5 CHD B:COH201 3.6 11.1 0.5 CHC B:COH201 3.6 14.2 0.5 CE1 B:TYR166 4.1 26.4 1.0 ND1 B:HIS83 4.2 12.4 1.0 OH B:TYR170 4.2 22.9 1.0 CG B:HIS83 4.3 11.5 1.0 C3C B:COH201 4.3 14.8 0.5 C3B B:COH201 4.3 10.6 0.5 C2D B:COH201 4.3 16.4 0.5 C3D B:COH201 4.3 17.1 0.5 C3C B:COH201 4.3 10.0 0.5 C3D B:COH201 4.3 15.1 0.5 C2D B:COH201 4.3 14.0 0.5 C2C B:COH201 4.4 14.6 0.5 C2B B:COH201 4.4 10.6 0.5 C3B B:COH201 4.4 15.0 0.5 C2A B:COH201 4.4 11.4 0.5 C3A B:COH201 4.4 10.6 0.5 C2B B:COH201 4.4 14.3 0.5 C2C B:COH201 4.4 9.8 0.5 C3A B:COH201 4.4 18.0 0.5 C2A B:COH201 4.4 19.1 0.5 CE2 B:TYR166 4.5 26.4 1.0 CZ B:TYR170 4.7 23.3 1.0 CE2 B:TYR170 4.7 21.4 1.0

J.C.Grigg, C.X.Mao, M.E.Murphy. Iron-Coordinating Tyrosine Is A Key Determinant of Neat Domain Heme Transfer. J.Mol.Biol. V. 413 684 2011.
ISSN: ISSN 0022-2836
PubMed: 21893067
DOI: 10.1016/J.JMB.2011.08.047